             [anglican.infcomp.network :refer :all]
             [anglican.inference :refer [infer]]
             [anglican.stat :refer [empirical-distribution collect-predicts collect-by collect-results]]
-            [helpers.gmm :refer [normalize]])
+            [helpers.gmm :refer [normalize]]
+            [rhizome.viz]
+            [clojure.string])
   (:use [anglican emit runtime]
         [gorilla-plot core]))
 
 (anglican.infcomp.core/reset-infcomp-addressing-scheme!)
 ;; @@
 ;; =>
-;;; {"type":"html","content":"<span class='clj-unkown'>#function[anglican.infcomp.core/reset-infcomp-addressing-scheme!$fn--26285$fn--26286]</span>","value":"#function[anglican.infcomp.core/reset-infcomp-addressing-scheme!$fn--26285$fn--26286]"}
+;;; {"type":"html","content":"<span class='clj-unkown'>#function[anglican.infcomp.core/reset-infcomp-addressing-scheme!$fn--26362$fn--26363]</span>","value":"#function[anglican.infcomp.core/reset-infcomp-addressing-scheme!$fn--26362$fn--26363]"}
+;; <=
+
+;; **
+;;; ## PDFA object
+;; **
+
+;; @@
+(defm new-pdfa [alphabet K transition emissiondist]
+  (let [alphabet (map str (seq alphabet))
+
+        states (range K)
+
+        edges (into {} (map (fn [state]
+                              [state (into {} (map #(vector % (transition state %))
+                                                   alphabet))])
+                            states))
+
+        probs (into {} (map (fn [state]
+                              [state (into {} (map (fn [[symbol prob]]
+                                                     [(str symbol) prob])
+                                                   (:categories (emissiondist state))))])
+                            states))]
+    {:edges edges
+     :probs probs}))
+;; @@
+;; =>
+;;; {"type":"html","content":"<span class='clj-var'>#&#x27;pdfa/new-pdfa</span>","value":"#'pdfa/new-pdfa"}
+;; <=
+
+;; @@
+(defn pdfa-states [pdfa]
+  (keys (:edges pdfa)))
+
+(defn pdfa-edges [pdfa]
+  (let [t (:edges pdfa)]
+    (into {} (map (fn [state]
+                    [state (vec (set (vals (get t state))))])
+                  (keys t)))))
+;; @@
+;; =>
+;;; {"type":"html","content":"<span class='clj-var'>#&#x27;pdfa/pdfa-edges</span>","value":"#'pdfa/pdfa-edges"}
+;; <=
+
+;; @@
+(defn pdfa-node->descriptor [pdfa]
+   (fn [node]
+     {:label (str node)}))
+
+(defn pdfa-edge->descriptor [pdfa]
+  (fn [state nextstate]
+    (let [edges (get-in pdfa [:edges state])
+          probs (get-in pdfa [:probs state])
+          
+          emissions (filter #(= nextstate (get edges %))
+                            (keys edges))
+          probs (into {}
+                      (map #(vector % (get probs %))
+                           emissions))]
+      {:label (clojure.string/join "|" (map #(format "%.3f%s"(get probs %) %)
+                                            emissions))})))
+;; @@
+;; =>
+;;; {"type":"html","content":"<span class='clj-var'>#&#x27;pdfa/pdfa-edge-&gt;descriptor</span>","value":"#'pdfa/pdfa-edge->descriptor"}
+;; <=
+
+;; @@
+(defn view-pdfa [pdfa]
+  (rhizome.viz/view-graph (pdfa-states pdfa)
+                          (pdfa-edges pdfa)
+                          :node->descriptor (pdfa-node->descriptor pdfa)
+                          :edge->descriptor (pdfa-edge->descriptor pdfa)))
+;; @@
+;; =>
+;;; {"type":"html","content":"<span class='clj-var'>#&#x27;pdfa/view-pdfa</span>","value":"#'pdfa/view-pdfa"}
 ;; <=
 
 ;; **

;; **

;; @@
(def alphabet "ABCDE")
(sample-observes-from-prior pdfa [(repeat 10 nil) alphabet])
;; @@
;; =>
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2} {:time-index 7, :observe-address O11, :observe-instance 7, :value 3} {:time-index 8, :observe-address O11, :observe-instance 8, :value 0} {:time-index 9, :observe-address O11, :observe-instance 9, :value 4}]"}
;; <=

;; @@
(defn combine-observes-fn [observes]
  (map :value observes))
;; @@
;; =>
;;; {"type":"html","content":"<span class='clj-var'>#&#x27;pdfa/combine-observes-fn</span>","value":"#'pdfa/combine-observes-fn"}
;; <=

;; @@
(def torch-connection (start-torch-connection pdfa [(repeat 10 nil) alphabet] combine-observes-fn))
;; @@
;; =>
;;; {"type":"html","content":"<span class='clj-var'>#&#x27;pdfa/torch-connection</span>","value":"#'pdfa/torch-connection"}
;; <=

;; @@
;; Stop the Torch connection


;; @@
(def num-particles 10)
(def csis-states (take num-particles (infer :csis pdfa [test-observations-str alphabet] :observe-embedder-input test-observations)))
;; @@
;; =>
;;; {"type":"html","content":"<span class='clj-var'>#&#x27;pdfa/csis-states</span>","value":"#'pdfa/csis-states"}
;; <=

;; @@
(first csis-states)
;; @@

;; @@
(categorical (vec (empirical-distribution (collect-results csis-states))))
;; @@
;; =>
;;; {"type":"list-like","open":"<span class='clj-map'>{</span>","close":"<span class='clj-map'>}</span>","separator":", ","items":[{"type":"list-like","open":"","close":"","separator":" ","items":[{"type":"html","content":"<span class='clj-keyword'>:categories</span>","value":":categories"},{"type":"list-like","open":"<span class='clj-vector'>[</span>","close":"<span class='clj-vector'>]</span>","separator":" ","items":[{"type":"list-like","open":"<span class='clj-vector'>[</span>","close":"<span class='clj-vector'>]</span>","separator":" ","items":[{"type":"list-like","open":"<span class='clj-map'>{</span>","close":"<span class='clj-map'>}</span>","separator":", ","items":[{"type":"list-like","open":"","close":"","separator":" ","items":[{"type":"html","content":"<span class='clj-keyword'>:edges</span>","value":":edges"},{"type":"list-like","open":"<span class='clj-map'>{</span>","close":"<span class='clj-map'>}</span>","separator":", 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;; <=

;; @@
(sample* (categorical (vec (empirical-distribution (collect-results csis-states)))))
;; @@
;; =>
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;; <=

;; @@
(def num-particles 1000)
(def test-obs "bbbbbbbbabbabbaaabbaaabbabbaaaaaabbaaabbabbaaabbbbbbabbaaabbbbbbbbbbabbbbbbbbbbabbaabbabbbbabbbbaaaaaaaaabbabbabbaaaabbabbaaaaabbaabbabbbbabbbbbbaabbabbabbbbabbabbbbbbaaabbabbbbaaabbbbaaabbbbbbabbaaaa")
(def is-states (take num-particles (infer :importance pdfa [test-obs alphabet])))
;; @@
;; =>
;;; {"type":"html","content":"<span class='clj-var'>#&#x27;pdfa/is-states</span>","value":"#'pdfa/is-states"}
;; <=

;; @@
(view-pdfa (sample* (categorical (vec (empirical-distribution (collect-results is-states))))))
;; @@
;; =>
;;; {"type":"html","content":"<span class='clj-nil'>nil</span>","value":"nil"}
;; <=

;; @@
(def num-particles 1000)
(def smc-states (take num-particles (infer :smc pdfa [test-observations-str alphabet] :number-of-particles 1000)))
(repeatedly 1 #(sample* (categorical (vec (empirical-distribution (collect-results smc-states))))))
;; @@
;; =>
;;; {"type":"html","content":"<span class='clj-var'>#&#x27;pdfa/num-particles</span>","value":"#'pdfa/num-particles"}
;; <=

;; @@

;; @@
